The Aftermath
by luckychi7
Summary: Naruto returns to Konoha with sage mode he learned from Lord Fukusaku only to find it in ruins caused by The Akatsuki leader Pain. Find out what happens the Jinchuriki in this alternate version with his fight with the rinnegan user.


**Author's Note: I have been thinking about allot of stuff relating to Naruto Shippuden, one idea that i came up with was if Naruto Shippuden/Naruto Part II had ended after the Pain Invasion Arc. That's how I came up with the story of The Aftermath. This also my first fanfic so let me know what you think of it. **

Obliterated

That was the best word to describe what Konoha has become thanks to Pain's Invasion on the village, but luckily before he could kill anybody else like Kakashi Hatake, Shizune, and Choza Akimichi, Naruto appeared before the rinnegan user and locked into destructive battle against him. He used as much chakra as he could in order to bring down Pain, Naruto even used his forbidden jutsu Rasen-Shuriken which destroyed five of six of the paths; Animal, Asura, Human, Petra, and Naraka. This was all thanks to Naruto's new sage mode which was able to perfect his Rasen-Shuriken.

However there was only still one more path left to destroy, The Deva Path which was Pain's most often used body. The Jinchuriki's sage mode ability disappeared which sent Lord Fukusaku, and Ma back to Mount Myoboku in order to recover their strength leaving Naruto to fight Pain all alone. Without sage mode Naruto was vulnerable to Pain in response he pinned the jinchuriki using the chakra disruption rods in order to take and extract the Nine Tailed Fox from him, but not before the violet haired byakugan user appeared came to Naruto's aid.

Hinata Hyuga's appearance in between his fight with Pain left Naruto shocked after she confessed her feelings for the yellow haired sage. The rinnegan user delivered the final blow to her by striking her down by using gravity force from the palm of his hand, and uses one of the chakra rods to kill her. Upon seeing his shy and sweet byakugan friend confess her feelings to him, and getting killed just to protect him left Naruto's anger to overwhelm him as he took the fourth tail form of the fox.

The battle from this point had shifted back to the Nine Tails Jinchuriki which had forced Pain to retreat from the village in order got him to use Chibaku Tensei. The result of this occurred after Naruto's anger helped him slip into the six tail form, which was at the point for the First Hokage's Necklace to try and surpress the chakra of the Nine Tails. However the six tails form was strong enough to destroy it which left Pain and the Jinchuriki end things, but he had used Chibaku Tensei which was able to allow the rinnegan user to create a Miniature Moon to trap the jinchuriki.

Naruto was locked within his own subconscious feeling lost in despair which allowed the Nine Tails Fox to take advantage of his pain, and convinced the host to destroy everything in the world by releasing the seal. A distort was caused in the seal, and while the strength of the miniature moon had helped trap the sixth tails form it took two level ahead to the second to last form before it could reach its full form. The eight tails form. it was just as massive as the Nine Tails with muscle tissue beginning to grow on the bones from the sixth tails form. This allowed him to partially break free from the sphere. Just as Naruto was about to release the seal of the fox from his mind the yellow flash of Konoha stopped Naruto before he could free the fox. Minato Namikaze The Fourth Hokage.

He spoke with Naruto, and revealed that he was Naruto's father. The yellow flash of the leaf explained to his son why he had sealed the nine tails within him, it was because The fox was let loose into Konoha by the mysterious masked man. All of a sudden Naruto remembers the encounter he had with a man wearing an orange colored lollipop like mask with a small hole to the left. Before he could say goodbye to his son, Minato redid the seal on Naruto's abdomen. The Yellow flash of the leaf told Naruto that he believes that the jinchuriki can succeed for what Jiraiya failed to do.

The eighth tail form of the fox stopped advancing to its full form as Naruto appeared as himself again instead of the Nine Tails. He continued his fight with Pain, and took the advantage of tricking Pain in using a Shinra Tensei on a dozen shadow clones. This gave Naruto enough time to eliminate The Deva Path with a rasengan, and uses one of the chakra receivers to track down the real Pain. Nagato.

It didn't take long for the yellow haired ninja to find Nagato a red haired emaciated man on some kind of machine and his partner Konan a blue haired woman wearing an akatsuki robe. Naruto still has some strive for vengeances towards the red haired decayed man for killing his sensei as well as his some of friends, along with causing the destruction of Konoha. Without hesitation Nagato used the power of the rinnegan in order to fight off against the yellow haired ninja by using smaller version of almighty push, but Naruto used the last amount of his chakra remaining to form a rasengan in order to put an end to the rinnegan user. Suddenly as both of their jutsus began to clash, the jinchuriki started to get images that had came from Nagato. His childhood up until now. Everything started to make sense to Naruto after understanding the pain Nagato had to go through, with the death of his parents along with being trained under Jiraiya, and finally the death of Yahiko which had become the second source to his pain. It lead to his insanity to subdue all of the the agenda that Yahiko had hoped to create for the Akatsuki in which Nagato took action of immediately. This helped Naruto realize the tragedy that Nagato had to go through.

"That explains everything" The jinchuriki sighed.

The rinnegan user shows a disgusted look towards Naruto "Explains what?"

"Your hatred towards Konoha, why you think suffering will only lead to peace. It's all because of what happened in your past" He explained to the emaciated red hair man.

Nagato still doesn't seem to care "Do you honestly think I give a damn?"

"Why else would you go this far into trying to obtain the tailed beasts" Naruto points out.

Knowing that there was no other explanation to back up on his quest for peace, Nagato gives up on trying and accepts the answer Naruto had given him. He knew that all of this could've been undone a long time ago.

"I will help you bring the world to peace Naruto Uzumaki" the red haired emaciated man said.

Konan is surprised "Nagato".

"Naruto is the child of the prophecy, and I will do what it takes to help him" Nagato said with a smile on his face then coughs more blood from his mouth.

"You don't have much time left Nagato" Konan said with a worried look on her face.

The red haired catches his breath "I know that's why I am going to use that jutsu" He said staring at the jinchuriki in the eye.

"What jutsu?' Naruto asked.

"Had I use this earlier I could revive all the people that died in Konoha, but now I can only revive one " Nagato explained using the last remaining portion of his chakra and life to revive somebody from Konoha before his eyes begin to fade to black ending his story.

"I pay my respects to you Nagato" Naruto said knowing he did the right thing, by not killing his brother in training.

"Jiraiya Sensei would be proud of him" Konan said.

"What are you gonna do now since Nagato is longer around?" Naruto asked a teary Konan.

"Since our Sensei, and Nagato have faith in you to bring the world to peace that gives me a good enough reason to have faith in you as well. But there is no purpose for me to be with the Akatsuki any longer so instead I will be going back to Amegakure and watch over its people, and I will do whatever I can to help you Naruto Uzumaki" Konan explained.

Before the jinchuriki left, the blue haired woman gives him paper flowers symbolizing the alliance between Konoha and Amegakure. After going through what he just went through with his battle let alone making the rinnegan user see the truth, Naruto is on the verge of passing out in the the middle of the forest, but suddenly a mysterious figure comes out from nowhere and takes Naruto as he begins to pass out.

"Naruto" a voice calls out.

He opens his eyes and closes them again "Naruto wake up".

This time Naruto wakes up with a headache "Wh.. What happened the last thing I remembered was walking in the middle of the forest and then I just passed out" He stops, and realizes everybody that survived the damage Pain caused have gathered around him plus he also realizes that his head has been lying on Sakura's lap.

"Well we're just glad your okay" Sakura said relieved to see her teammate awake.

He realizes something once he gets up from Sakura's lap "Wait a minute where is Kakashi Sensei, Shizune, and Grandma Tsunade. Would anybody please tell me?"

The pink haired kunoichi and the other survivors there showed a sad expression on their face.

"They didn't make it" Yamato answered.

The news of their death shocks the jinchuriki as he had hope that they would make it out of this invasion, and couldn't believe that they are dead like all the other survivors in Konoha.

"Did anyone else make it?" Naruto asked hoping that somebody survived.

"There was one that made it out. right over there" Kiba said pointing as somebody brought an unconscious person forward.

Naruto was shocked once he realized who it was "Hinata"

"She was the only person out of the five people that made it" Sakura explained.

"But how come she isn't awake?" Naruto worried about the violet haired Hyuga.

"It's because she is in a coma Naruto" Ino said walking up to Naruto.

He couldn't believe what the blonde told him "What did you say Ino?"

"She had woken up for a small amount of time, but then she shut her eyes, and didn't move after that. Ino and I tried everything we could, but we came to the conclusion that Hinata was stuck in a coma" Sakura explained to her spiky yellow haired teammate.

Naruto is relieved that Hinata is alive for the most part "I think there is something we have all forgotten about" Sai called out.

"What's that?" Kiba asked.

"Konoha needs a Hokage" Sai said.

Everyone was shocked because they had forgotten about that since the Fifth Hokage is now dead.

"The age requirement for Hokage is eighteen years old, and our best jonin that qualify for Hokage are already dead. Kakashi was one shinobi that could've been next in line" Homura the male elder of Konoha who was also friends with the third hokage explained.

Koharu the female elder of Konoha who learned from The Second Hokage appears before The Konoha Nine "Then our final choice was gonna be Danzo, but he was nowhere to be found after the devastation of the village" She explained.

Everyone tries to think of a person that would be a great choice to be the next hokage until Konohamaru calls out "Why do you guys seem so worried about finding a person to be Hokage when you've already got one".

"Who might that be Konohamaru?" Sakura asked curious to know who he has in mind.

Third Hokage's grandson sighed because nobody could figure out so he points out the person he had in mind "Naruto Uzumaki"

The jinchuriki was shocked to hear Konohamaru say that about finding somebody to take the late Fifth Hokage's place. This had also started a gossip around all the survivors in Konoha trying to decide.

Homura argued "Did anybody forgot what Naruto was. The Nine Tails Jinchuriki. The beast that attacked and tried to destroy our village sixteen years ago is sealed away inside of him".

"Besides you should all remember it was thanks to The Fourth Hokage who had sacrificed his life in order to seal away the beast that saved all of you back then. You would want somebody that carries something dangerous to be your Hokage. The final point I have with this is the fact that Naruto is only sixteen years old" Koharu explained backing up Homura's argument.

The people of Konoha now have mixed opinions whether or not Naruto should be Hokage, and besides the point he is only two years under Age requirement to be qualified. Naruto knows that he can't be silent about this because Konohamaru is right about one thing there is nobody else better than himself "There is something the elders are hiding from all of you".

The elders look at him like as if there is nothing that Naruto doesn't know about, until they notice the smirk on his face "What do you know boy tell us?" Homura yelled.

"The nine tails jinchuriki standing in front of you is none other than the son of The Fourth Hokage" He said revealing the truth.

"The Son of who now?" Shikamaru said.

This announcement comes as a shock to The elders, the people of Konoha, Sai, Shikamaru, Ino, Neji, Lee, Tenten, Choji, Kiba, Sakura, and all shinobi that herd Naruto.

"No way you're the son of the Fourth Hokage" Sakura said with a shocked tone in her voice.

Koharu gives Naruto with a snake like look in her eye "How? When did you know? Answer Nine Tails"

He explains of how he discovered the truth about being the son of The Yellow Flash. This comes as a disappointment to the elders.

"Age shouldnt even be a big deal, all that matters is that Naruto defeated the leader of the Akatsuki. He is the hero of Konoha" a villager called out supporting Naruto.

"Didn't you see the destructive powers of the fox he released. He is also to blame for the destruction of Konoha" Homura yelled trying to make everyone understand.

Naruto starts to get a laugh out of Homura's argument "What the the hell are you laughing about Jinchuriki?" Koharu yelled.

"The fact that you two would hide something so dark as this to me had I known maybe I would've understood back then, but I guess there were some things that couldn't have been revealed. Plus knowing the two of you there are more stuff you must've kept away then The Fourth Hokage being my father" Naruto said giving them his glare.

Sakura feels bad for what Naruto is going through, and she knows that she can't just sit around and watch Naruto hurt his throat "I don't think we should even trust them at all".

"I agree with Sakura" Rock Lee said standing by her side alongside Naruto.

Neji, Tenten, Shikamaru, Ino, Choji, and Sai also support Sakura. This eventually follows down to the other survivors of Konoha like Kurenai, Yamato, Guy, and Ebisu sensei.

"You haven't heard the last of us Nine Tailed Fox" The Elders said before they disappear from the wasteland of Konoha.

Everybody is just standing there wondering what to do since the Elders have left Konoha now. Naruto focuses his attention on Yamato as he gives out a small nod "You know what to do Yamato"

"Right" the wood style user said placing his hands on the ground as buildings rise upfrom the ground.

"At this rate Konoha will be back in no time" one of the ninja's said cheerfully.

An exhausted Yamato replies back "If only it were that easy"

Shikamaru places his hand on the yellow haired Uzumaki "I think its time we pay our respects to those that didn't make it"

While the funerals of the deceased shinobis needed some time to set before it could begin, Sasuke is seen sitting in the chair where the Akatsuki meeting would normally be.

He thinks back to his fight with his older brother Itachi Uchiha, and learning the truth about him from Madara Uchiha.

"You seem bothered by something?" Madara asked.

Sasuke gives Madara an evil smirk on his face "No I am just ready to put an end to Konoha"

"It appears you are already too late" a voice called.

The Zetsu appears from the ground which doesn't surprise the two of them "What do you mean I am too late" Sasuke yelled.

"Pain had already destroyed Konoha during his fight with The Nine tails Jinchuriki" The Zetsu revealed.

"What was the battle's outcome?" Madara asked wanting to know.

The Black Zetsu answers "Pain was defeated".

"And The Nine Tails Jinchuriki was chosen to be the new Hokage of Konoha" The White Zetsu finished off the sentence.

"What did you say?" Sasuke asked with a shocked reaction on his face.

"Naruto Uzumaki is The New Hokage of Konoha" The White Zetsu said again.

Sasuke couldn't believe that Naruto Uzumaki, his rival who was once his best friend, has finally completed his dream to become the Hokage of Konoha. But for some reason he starts laughing for no reason "Naruto you fool. Do you honestly think that you're above the Uchiha just because you finally completed your dream of becoming Hokage. No it's quite the opposite old friend. it furthers my hatred towards Konoha even more, and I'll start with the three elders" He said changing his eyes into the mangekyo sharingan.

"Sasuke your goal may take less time to occur" Madara said.

He looked at the masked man with an expectation look on his face "What do you mean by that Madara?".

The Orange Masked Man time spaces Danzo Shimura from the seal dimension to Sasuke which intrigues him "How were you able to get him" Sasuke asked.

Madara explains the story of how he had gotten Danzo. It was before Pain invades Konoha. Danzo was keeping his eye on the Anbu, The Elders, and Tsunade. Then Madara Uchiha appeared before the old man and locked him into a battle that had took place below the village. Madara was pushed to his limit and activated his secret most dangerous which would place Danzo in an genjutsu that couldn't be broken. Only Madara Uchiha can undo the genjutsu. Using this to his advantage Madara took Danzo and placed him in the sealed dimension.

"How long would it take for him to regain consciousness once you undone the genjutsu you placed him under" Sasuke asked using this to his advantage to gain the answers he seeks.

"He'll awaken, but conscious wise it'll take him about an hour for him to know that we are there" Madara explained.

Sasuke shows a grin on his face "Undo the genjutsu now".

Madara undos the jutsu "Go on, obtain the answers you seek".

"Was the Uchiha Massacre really just mission that Itachi had to carry out by Konoha?"Sasuke asked grabbing Danzo by his shirt.

An tired exhausted Danzo replies with "Yes Konoha assigned a mission that night".

"That's all I need to hear" Sasuke yelled throwing Danzo next to a wall "Amaterasu" a trail of black flames come from the black haired Uchiha as it covers and kills Danzo. The results of using Amaterasu also puts an effect on Sasuke's eye.

The Black Zetsu grunts "Foolish child doesn't he know what affect that'll do to his eyes".

"I guess not" White Zetsu said after witnessing what Sasuke just did to Danzo.

Madara Uchiha was intrigued by Sasuke's one shot blow to Danzo "Sasuke you do realize what the Mangekyo Sharingan can do to your eyesight right?".

"Yes I do, and that's why i think now would be the perfect time to implant Itachi's eyes into my own if i want to become stronger then the Hokage" Sasuke said covering his left eye which is dripping out blood.

Madara is pleased by the fact that the young Uchiha wants to do whatever it takes to achieve his goal "Just know obtaining the eternal mangekyo sharingan takes about seven months to sync in with your own, but the downside to this is that it'll take about two years for its full powers to be unleashed, so until then I will train you get stronger".

A laughter comes from the young Uchiha "That's fine because then it'll be alot easier to destroy Konoha".

Back in Konoha

The Funeral for those that didn't make it out of Pain's attack is about to begin. There were four coffins placed out on a board each having a picture on top of it. Kakashi's was on the far the right, next to his was Shizune's, then came Choza Akimichi, and finally Tsunade's Coffin. Naruto is wearing a white short sleeve coat with small flame diesels on along with his normal clothes underneath the coat. He is on stage holding a microphone amongst the other surviving Konoha shinobi ready to make his speech.

"Not too long ago Konoha was attacked by The Akatsuki Leader Pain a man who had possessed the rinnegan, and was after me The Nine Tails Jinchuuriki. We fought our way through to try and stop him, and as a result most of our great shinobis died fighting for our existence for Konoha" tears started to come out of Naruto's eyes, but still continues to talk "Our Friends and Families let alone The Fifth Hokage. Kakashi Hatake. Shizune. Choza Akimichi. And to All our other Shinobis that didn't make it from this devastation. Let us give them respect and honor for what they have done for Konoha. And as The Sixth Hokage I will be sure to keep this village safe from anybody that wants to see us shinobi dead. From this day on we will rebuild from the ground up to revive Konoha".

Everybody cried, and cheered for Konoha Sixth Hokage's speech and respects to those that died during the Attack on their village. When the sun is about set, Naruto is seen placing the paper flowers made from Konan along with a copy of Jiraiya's book "Tale of a Gutsy Ninja" by a tree standing right next to the temporary Hokage Mansion.

"I'll never forget what you taught me pervy sage" Naruto said remembering his sensei.

a voice calls out "Hey Naruto"

He turns around, and it's Sakura "Oh hey Sakura. Has Hinata recovered by any chance?".

"Not yet Naruto she is still in a coma" Sakura said giving him the update.

Naruto seems disappointed "Oh okay thanks for letting me know."

"I guess you've finally gotten what you always wanted" She said giving him a quick smile.

Although Naruto doesn't seem happy about it "Yeah I did, but i wasn't able to save anybody. Kakahi, Grandma Tsunade, and the other people that died today".

Sakura gives Naruto now the Sixth Hokage a hug "I know Naruto, it's hard seeing people you care about go away especially me. Lady Tsunade taught me everything I needed to know to become a medical ninja let alone a better shinobi"

"Pervy Sage had also did the same with me" Naruto chuckled a bit.

Naruto lets go of hugging Sakura as something was on his mind "What's wrong?"

"It's just that I still have to keep my promise to you about bringing Sasuke back to Konoha" Naruto said giving the pink haired kunoichi a smile.

**End of Naruto Part II **


End file.
